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I bought a Trek Project one in 2008 with Dura-Ace and compact gearing.
This bike came with Bontrager Carbon Fiber cranks and as it turns out, the 50 & 36t chainrings are Sram. Later that year, my bike shop ordered up a new Sram cassette 11-28 teeth (pie plate) so I could ride some steeper hills. At the time, Shimano did not offer a Dura-Ace 11-28 cassette. Everything worked great for the next 18,000 miles or so until I started getting some noise from the drive train. I change the chain at least twice a year and have always used Dura-Ace 10 speed chain.

I just put a brand new Dura-Ace chain on and I'm getting some slipping on the big ring. The chain seems to be riding up on top of the teeth at times so I'm certain the chainrings are worn. I am shopping for new ones, and most likely a new cassette. I would like to have everything Dura-Ace but I have "Dura-Ace Taste" on a 105 budget.

My questions: Should I have been running Sram chains since the drive train is / was mostly Sram?
Is is kosher to run Sram rings in the front with a Dura-Ace cassette in the back?
If so which chain should I use?

D-A chain should be fine on a SRAM drivetrain. You should check for chain stretch often. The chain should be replaced by the time any one-foot interval has stretched to 12 1/16 inches. Don't guess, measure closely at least 3 different intervals. Chains do not necessarily stretch evenly. Mine don't.

Intermixing is just fine like that, though if you have 18k miles on those parts, they're worn out. The SRAM cassettes aren't good for that long. You can easily get brand new Ultegra 11-28s on eBay for about $70.